Interpretive Summary: The gastrointestinal tracts (GIT) of beef cattle are colonized by microorganisms that profoundly impact animal physiology, nutrition, health, and productivity. The GIT microbiota potentially impact food safety via pathogen shedding by interacting with organisms such as Salmonella and Escherichia coli O157:H7 and competing for resources in the GIT. Cattle intestinal microbiota also play an important role in methane emissions, with U.S. beef cattle alone contributing an estimated 3.87 million metric tons of methane into the environment each year, both from rumen and large-intestine fermentations. Despite the potential contributions of the beef cattle GIT microbiota to animal health, food safety, and global warming, these communities remain poorly characterized. We have, therefore, characterized fecal bacteria from six feedlot cattle using gold-standard, full-length DNA sequencing of more than 11,000 bacteria. Our findings, in addition to those from other studies, identify a core set of bacteria that can be found in cattle feces. Our study also revealed that there is considerable animal-to-animal variation in the bacteria found in each animal, even though the cattle were all of the same gender, breed, and age, and even though they had all been housed together and fed the same diet for over two months. This is the most comprehensive study to date of the bacteria in cattle feces using these gold-standard methods.

Technical Abstract:
The intestinal microbiota of beef cattle are an essential component of animal health and productivity. Here we present a survey of fecal bacteria from six beef cattle generated by near full-length sequencing of 11,171 16S rDNA genes. Deep sequencing revealed considerable variation in the phylotype composition of individual libraries.